This preliminary report details the results of looking for pathway enrichment in each of the groups of genes produced by hierarchical clustering of the drug perturbations. I’ve cut the the data into 15, but this value can be changed if we decide on a different value. Otherwise, this analysis focuses on enriched pathways in the MSigDB database. Specifically, this analysis uses the Hallmark segment from: https://www.gsea-msigdb.org/gsea/msigdb.
As for this report, the panel on the left is sorted by the number of dark kinases in the cluster and displays both the number of pathway hits and dark kinases in the cluster. The number of each cluster is arbitrary. The entry for each cluster displays the kinases associated with the cluster along with the number of non-kinases genes. Below this table are the pathways that passed the enrichment analysis at the 0.01 false discovery rate level. I also corrected for running this analysis for all 15 clusters.
Overall, 47 pathways are enriched in at least one of the following clusters. Of these pathways 4 are only hit once. The following pathways are seen in two or more clusters:
The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.
| gene_type | info |
|---|---|
| Dark Kinase (27) | CAMKK1, CDK11A, CDK12, CDK17, CDKL1, CLK3, COQ8A, CSNK1G1, CSNK2A2, DYRK2, HIPK1, MAST2, NEK1, NEK4, NEK7, PAN3, PDIK1L, PHKG2, PIP5K1A, RIOK3, SCYL1, STK19, TAOK1, TESK1, TLK1, TLK2, ULK4 |
| Light Kinase (61) | ABL2, ADPGK, ARAF, ATM, AURKB, BAZ1A, BAZ1B, BRD4, BTK, BUB1, CAMK2A, CAMK2G, CDK1, CDK2, CDK3, CHEK1, CLK1, CSK, DDR2, DGKE, DGKZ, FER, GRK2, GRK7, GSK3A, GTF2F1, HKDC1, HSPB8, IRAK3, LYN, MAP2K7, MAP3K6, MAP4K4, MAPK6, MAPK7, MAPK8, MASTL, MELK, MLKL, MYLK2, NEK2, PAK1, PAK2, PASK, PI4KB, PIK3C3, PLK4, RPS6KA5, SIK1, SIK1B, SLK, SMG1, SRPK1, STK10, STK35, STK4, TPTEP2-CSNK1E, TTN, TYRO3, WEE1, YES1 |
| Non-kinase Count | 2741 |
| label | pval | fdr | signature | geneset | overlap | hits |
|---|---|---|---|---|---|---|
| HALLMARK_G2M_CHECKPOINT | 0.0e+00 | 0.0e+00 | 2829 | 200 | 79 | AMD1,ATRX,AURKB,BRCA2,BUB1,CASP8AP2,CCNA2,CCNB2,CCNT1,CDC25A,CDC27,CDC6,CDK1,CENPA,CHEK1,CHMP1A,CTCF,CUL1,CUL3,CUL4A,CUL5,DKC1,DR1,E2F1,E2F2,E2F3,ESPL1,EWSR1,GINS2,GSPT1,HMGN2,HMMR,HNRNPD,HNRNPU,HSPA8,ILF3,INCENP,KIF2C,KIF5B,KMT5A,KPNA2,KPNB1,LMNB1,MCM3,NASP,NEK2,NSD2,NUP50,NUSAP1,ODF2,ORC6,PDS5B,PLK4,PML,POLE,PRC1,RACGAP1,RAD21,RAD54L,RBL1,RBM14,RPA2,RPS6KA5,SFPQ,SMARCC1,SMC2,SMC4,SRSF2,SS18,STAG1,TENT4A,TMPO,TNPO2,TOP2A,TPX2,TRA2B,TRAIP,TROAP,UBE2C |
| HALLMARK_E2F_TARGETS | 0.0e+00 | 0.0e+00 | 2829 | 200 | 75 | ANP32E,ATAD2,AURKB,BRCA2,BRMS1L,CCNB2,CDC25A,CDK1,CENPM,CHEK1,CNOT9,CTCF,CTPS1,DCK,DEK,DEPDC1,DIAPH3,ESPL1,GINS4,GSPT1,HMGB2,HMMR,HNRNPD,ILF3,ING3,IPO7,KIF2C,KPNA2,LMNB1,LUC7L3,MCM3,MCM4,MCM7,MELK,MMS22L,MSH2,NAP1L1,NASP,NUDT21,NUP153,NUP205,ORC6,PCNA,PDS5B,PHF5A,PLK4,POLD3,POLE,POP7,PSMC3IP,RACGAP1,RAD1,RAD21,RAD51AP1,RAN,RFC1,RNASEH2A,RPA2,SLBP,SMC3,SMC4,SNRPB,SPC24,SRSF2,STAG1,TCF19,TMPO,TOP2A,TRA2B,TUBB,UBE2T,UBR7,UNG,USP1,WEE1 |
| HALLMARK_MYC_TARGETS_V1 | 0.0e+00 | 0.0e+00 | 2829 | 200 | 53 | CCNA2,CDK2,COX5A,CTPS1,CUL1,CYC1,DEK,EEF1B2,EIF4A1,EIF4G2,GSPT1,HNRNPA1,HNRNPA2B1,HNRNPA3,HNRNPD,HNRNPU,IFRD1,KPNA2,KPNB1,MCM4,MCM7,MRPL9,NAP1L1,PABPC1,PCNA,PHB2,PSMA1,PSMA2,PSMA7,PSMB2,PSMC4,PSMC6,PSMD1,PSMD8,PWP1,RAN,RNPS1,RPL22,RRM1,RRP9,SET,SLC25A3,SMARCC1,SNRPA,SNRPA1,SRPK1,SRSF2,TRA2B,UBA2,USP1,VBP1,VDAC1,VDAC3 |
| HALLMARK_MITOTIC_SPINDLE | 0.0e+00 | 0.0e+00 | 2829 | 199 | 49 | ALMS1,ARFGEF1,ATG4B,BIN1,BRCA2,BUB1,CCNB2,CDC27,CDK1,CDK5RAP2,CEP57,CEP72,CKAP5,CLIP1,CNTRL,CNTROB,CTTN,DOCK2,EPB41L2,ESPL1,HOOK3,INCENP,KIF1B,KIF2C,KIF5B,LMNB1,NEK2,NF1,NUSAP1,PCGF5,PCM1,PCNT,PPP4R2,PRC1,RAB3GAP1,RACGAP1,RALBP1,RASA2,RFC1,RICTOR,SMC3,SMC4,STAU1,TLK1,TOP2A,TPX2,TSC1,WASF1,WASF2 |
| HALLMARK_PROTEIN_SECRETION | 0.0e+00 | 0.0e+00 | 2829 | 96 | 28 | ABCA1,ANP32E,AP1G1,AP2B1,AP3B1,ARCN1,ARFGEF1,ARFGEF2,ATP6V1H,CLTA,CLTC,DNM1L,ERGIC3,GALC,GLA,KIF1B,PPT1,RAB14,RER1,SCAMP3,SOD1,STAM,STX16,TMED2,VAMP3,VAMP7,VPS45,VPS4B |
| HALLMARK_OXIDATIVE_PHOSPHORYLATION | 0.0e+00 | 0.0e+00 | 2829 | 200 | 41 | ABCB7,ACO2,ATP5F1B,ATP5MG,ATP5PB,ATP6V1G1,ATP6V1H,CASP7,COX5A,CS,CYC1,ECI1,GLUD1,GRPEL1,HSD17B10,HSPA9,IDH3B,ISCA1,MFN2,MRPL15,MRPS15,MRPS30,MTRF1,NDUFA9,NDUFS3,NDUFS7,NDUFS8,PDHA1,PDHX,PHB2,SLC25A3,SLC25A5,SUCLG1,SUPV3L1,TIMM10,TIMM50,UQCRC2,UQCRH,VDAC1,VDAC2,VDAC3 |
| HALLMARK_DNA_REPAIR | 0.0e+00 | 0.0e+00 | 2829 | 150 | 34 | ADRM1,ALYREF,ARL6IP1,BRF2,DCTN4,DDB1,DGCR8,ELL,ELOA,ERCC8,GTF2F1,GTF2H1,NT5C3A,NUDT21,PCNA,POLD3,POLL,POLR1D,POLR2A,POLR3C,POM121,RAD51,RAD52,RAE1,RPA2,SF3A3,SNAPC5,SRSF6,SUPT5H,TAF1C,TMED2,UPF3B,ZNF707,ZWINT |
| HALLMARK_MTORC1_SIGNALING | 0.0e+00 | 0.0e+00 | 2829 | 200 | 36 | ABCF2,ACACA,ACTR3,ATP2A2,BUB1,CDC25A,CYB5B,EEF1E1,GBE1,GLA,GMPS,GSR,GTF2H1,HSPA9,IFRD1,MCM4,NFKBIB,NFYC,NUP205,PPP1R15A,PSMA3,PSMB5,PSMC2,PSMC4,PSMC6,PSMD12,RAB1A,RIT1,RRP9,SEC11A,SLC7A11,SORD,SSR1,TMEM97,UBE2D3,UNG |
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE | 0.0e+00 | 0.0e+00 | 2829 | 113 | 26 | ATF4,BAG3,CNOT2,CNOT4,CNOT6,DCP1A,DCP2,DKC1,EDC4,EIF4A1,EXOSC10,EXOSC4,EXOSC5,EXOSC9,FUS,HSPA9,KHSRP,KIF5B,NFYB,PAIP1,RRP9,SEC11A,SLC30A5,SRPRB,SSR1,TATDN2 |
| HALLMARK_PI3K_AKT_MTOR_SIGNALING | 1.0e-07 | 4.0e-07 | 2829 | 105 | 22 | ACACA,ACTR3,AKT1S1,ATF1,CAB39L,CDK1,CDK2,CLTC,E2F1,ECSIT,FGF22,GNGT1,GRK2,MAPK8,NFKBIB,PLCG1,PPP2R1B,PTPN11,RIT1,SFN,TRAF2,UBE2D3 |
| HALLMARK_MYC_TARGETS_V2 | 6.0e-07 | 2.5e-06 | 2829 | 58 | 15 | EXOSC5,GRWD1,MAP3K6,MCM4,NIP7,PES1,PLK4,PPAN,PPRC1,PUS1,RRP9,SORD,SUPV3L1,TMEM97,UNG |
| HALLMARK_HEME_METABOLISM | 3.2e-06 | 1.4e-05 | 2829 | 200 | 29 | ADIPOR1,CCDC28A,CDC27,CIR1,CROCCP2,DCUN1D1,E2F2,EZH1,FBXO7,FOXJ2,GAPVD1,GMPS,GYPA,ICAM4,ISCA1,MKRN1,MOCOS,NARF,NEK7,NUDT4,RANBP10,RBM5,RIOK3,SLC25A38,SLC4A1,SLC6A9,SLC7A11,SYNJ1,TFDP2 |
| HALLMARK_SPERMATOGENESIS | 7.3e-06 | 2.8e-05 | 2829 | 135 | 22 | BUB1,CCNB2,CDK1,CLVS1,COIL,CSNK2A2,DMC1,IL12RB2,KIF2C,MAST2,MEP1B,MLLT10,NCAPH,NEK2,OAZ3,PARP2,PHKG2,PIAS2,SIRT1,TOPBP1,VDAC3,ZC3H14 |
| HALLMARK_UV_RESPONSE_UP | 3.0e-05 | 1.1e-04 | 2829 | 158 | 23 | AGO2,AMD1,BID,CASP3,CDK2,CLTB,CYB5B,DNAJA1,DNAJB1,EIF5,GRPEL1,HNRNPU,KLHDC3,LYN,NXF1,PARP2,PPIF,PPP1R2,PPT1,PSMC3,SHOX2,SPR,TYRO3 |
| HALLMARK_ADIPOGENESIS | 1.8e-04 | 5.5e-04 | 2829 | 200 | 25 | ABCA1,ACO2,ALDH2,ARAF,BAZ2A,CMPK1,CS,CYC1,ELMOD3,GBE1,GHITM,GRPEL1,HSPB8,LEP,MRPL15,NDUFS3,PEX14,PFKFB3,RIOK3,RREB1,SAMM50,SOD1,SUCLG1,UBC,UCK1 |
| HALLMARK_P53_PATHWAY | 1.8e-04 | 5.5e-04 | 2829 | 200 | 25 | CCNK,CDKN2AIP,COQ8A,DNTTIP2,FBXW7,HINT1,IP6K2,KLF4,MDM2,MXD1,NOTCH1,NUDT15,PCNA,POM121,PPP1R15A,PRKAB1,RB1,RCHY1,RNF19B,SFN,SLC19A2,SLC3A2,SLC7A11,TRAF4,WWP1 |
The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.
| gene_type | info |
|---|---|
| Dark Kinase (19) | CAMK1D, CAMKV, CDKL3, DYRK1B, LMTK2, LMTK3, MAP3K15, MAPK15, MARK1, MKNK1, NEK5, PIK3C2B, PIP5K1B, SBK1, SCYL2, STK3, TESK2, TSSK1B, VRK3 |
| Light Kinase (46) | ACVR1C, ACVR2A, ACVRL1, ANKK1, BMP2K, BMX, CAMK2B, CAMK4, CDK9, CSF1R, DAPK1, DAPK2, DCLK1, EPHA6, EPHB2, EPHB3, FGFR1, FGFR2, FGFR3, FGFR4, FLT4, HCK, ITK, JAK2, KALRN, KSR1, KSR2, MAP2K3, MAP2K6, MAP4K1, MAPK10, MAPK11, MAST1, MATK, PI4KAP2, PRKCG, PRKCZ, PRKD2, PTK2, RPS6KA3, SGK2, SRPK2, STK26, STYK1, TAF1L, TXK |
| Non-kinase Count | 1748 |
| label | pval | fdr | signature | geneset | overlap | hits |
|---|---|---|---|---|---|---|
| HALLMARK_APICAL_JUNCTION | 0.0e+00 | 0.0e+00 | 1813 | 200 | 31 | ACTN2,ADAM23,AMIGO1,ATP1A3,CADM2,CALB2,CD209,CD34,CD86,CDH1,CDH15,CDH3,CNTN1,DHX16,DSC3,ICAM2,JAM3,KCNH2,LAYN,MAPK11,NECTIN2,NFASC,NRXN2,PARD6G,PPP2R2C,PTK2,SLC30A3,SYMPK,TJP1,TRO,VCAN |
| HALLMARK_SPERMATOGENESIS | 0.0e+00 | 1.0e-07 | 1813 | 135 | 22 | ACE,ALOX15,CAMK4,CHRM4,CNIH2,CRISP2,DCC,DDX25,DMRT1,GAD1,GSG1,GSTM3,JAM3,MAP7,MLF1,NOS1,SCG3,SEPTIN4,STAM2,STRBP,TNNI3,TUBA3C |
| HALLMARK_ALLOGRAFT_REJECTION | 0.0e+00 | 1.0e-07 | 1813 | 200 | 27 | ACHE,ACVR2A,CD1D,CD3D,CD40,CD74,CD86,CDKN2A,CRTAM,GPR65,IL11,IL12A,IL16,IL2RB,IL7,INHBB,ITGAL,ITK,JAK2,MAP4K1,NOS2,PRKCG,RPL3L,STAB1,STAT4,UBE2D1,WAS |
| HALLMARK_ESTROGEN_RESPONSE_LATE | 0.0e+00 | 1.0e-07 | 1813 | 200 | 27 | AFF1,ANXA9,CACNA2D2,CDH1,CYP26B1,DHRS2,DNAJC1,EMP2,FGFR3,IGSF1,JAK2,KCNK5,KLK10,KLK11,LSR,LTF,MOCS2,NPY1R,OLFM1,PDLIM3,PLAC1,PRKAR2B,S100A9,SLC1A4,SLC29A1,SULT2B1,TMPRSS3 |
| HALLMARK_COMPLEMENT | 0.0e+00 | 2.0e-07 | 1813 | 200 | 26 | ACTN2,ATOX1,CLU,CPM,CR2,F5,FCN1,GCA,GRB2,HNF4A,HPCAL4,ITGAM,JAK2,KLK1,KLKB1,LGMN,LTF,MMP13,PIK3R5,PLA2G4A,PLAT,S100A9,SCG3,SH2B3,SPOCK2,WAS |
| HALLMARK_KRAS_SIGNALING_DN | 1.0e-07 | 7.0e-07 | 1813 | 200 | 25 | ABCG4,C5,CAMK1D,CLSTN3,CPEB3,CYP39A1,DCC,FGFR3,HSD11B2,IGFBP2,KCND1,KCNMB1,KCNN1,KLK7,NOS1,NR6A1,RYR1,SIDT1,SLC30A3,SLC5A5,SLC6A14,TAS2R4,TCF7L1,TFCP2L1,TNNI3 |
| HALLMARK_IL2_STAT5_SIGNALING | 1.1e-06 | 6.0e-06 | 1813 | 199 | 23 | ABCB1,AHR,CD83,CD86,CST7,EOMES,ETFBKMT,FAM126B,GALM,GPR65,GUCY1B1,HUWE1,IL1R2,IL2RB,IL3RA,ITGA6,ITIH5,LRRC8C,MAP6,SELL,TLR7,TNFRSF8,TNFSF10 |
| HALLMARK_ESTROGEN_RESPONSE_EARLY | 1.2e-06 | 6.0e-06 | 1813 | 200 | 23 | AFF1,ANXA9,CALB2,CYP26B1,DHRS2,ENDOD1,INHBB,JAK2,KAZN,KCNK5,KLK10,NPY1R,OLFM1,PDLIM3,PODXL,RAB17,REEP1,SLC1A4,SULT2B1,SYBU,TBC1D30,TMPRSS3,UGCG |
| HALLMARK_INFLAMMATORY_RESPONSE | 1.2e-06 | 6.0e-06 | 1813 | 200 | 23 | ACVR2A,ADGRE1,AHR,CCRL2,CD40,CD70,CYBB,FFAR2,IL2RB,LAMP3,NMUR1,NPFFR2,OPRK1,P2RX7,PIK3R5,PTAFR,PTGER4,SELL,SEMA4D,SLC28A2,STAB1,TNFSF10,TNFSF15 |
| HALLMARK_MYOGENESIS | 1.2e-06 | 6.0e-06 | 1813 | 200 | 23 | ACHE,ACTN2,CAMK2B,CLU,CNN3,DAPK2,EIF4A2,EPHB3,FKBP1B,GNAO1,KCNH2,KLF5,MAPRE3,MYL2,NCAM1,NOS1,PTGIS,REEP1,RYR1,SLN,SPDEF,SPTAN1,TNNT2 |
| HALLMARK_HEDGEHOG_SIGNALING | 4.1e-06 | 1.9e-05 | 1813 | 36 | 9 | ACHE,CRMP1,GLI1,HEY2,NKX6-1,NRP2,SCG2,SLIT1,TLE3 |
| HALLMARK_INTERFERON_GAMMA_RESPONSE | 1.4e-05 | 5.4e-05 | 1813 | 200 | 21 | CD38,CD40,CD74,CD86,CIITA,IL2RB,IL7,ITGB7,JAK2,OASL,PELI1,PLA2G4A,SAMHD1,SLAMF7,ST3GAL5,STAT4,TDRD7,TNFSF10,TOR1B,TRAFD1,ZNFX1 |
| HALLMARK_KRAS_SIGNALING_UP | 1.4e-05 | 5.4e-05 | 1813 | 200 | 21 | ABCB1,ACE,CBL,EPHB2,EVI5,FLT4,GPRC5B,GUCY1A1,IL33,KIF5C,MAP4K1,MAP7,MMD,PIGR,PLAT,SCG3,TMEM100,TMEM176B,TNNT2,TOR1AIP2,TPH1 |
| HALLMARK_HEME_METABOLISM | 4.5e-05 | 1.6e-04 | 1813 | 200 | 20 | ACSL6,ADD2,ATG4A,BMP2K,BTRC,CDR2,ENDOD1,MAP2K3,MPP1,PSMD9,RAP1GAP,RBM38,RCL1,SLC30A10,SLC66A2,SPTA1,SPTB,TMCC2,TSPAN5,XK |
The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.
| gene_type | info |
|---|---|
| Dark Kinase (14) | CDK19, DSTYK, HIPK3, LRRK1, MAP3K10, MARK4, NEK11, PIP4K2C, PIP5K1C, RPS6KC1, SBK3, SRPK3, STK38L, TTBK2 |
| Light Kinase (32) | AAK1, ABR, ACVR1, BRD2, CAMK2D, CSNK1D, DGKD, EIF2AK3, FRK, GSK3B, HK1, ILK, INSR, JAK1, LATS2, MAP2K2, MAP3K8, MAPK1, MAPKAPK2, MST1R, MYLK3, MYLK4, NRBP1, NUAK1, PEAK1, PI4K2A, PINK1, SIK3, TAOK3, TGFBR1, TRPM7, ULK1 |
| Non-kinase Count | 1183 |
| label | pval | fdr | signature | geneset | overlap | hits |
|---|---|---|---|---|---|---|
| HALLMARK_CHOLESTEROL_HOMEOSTASIS | 0.0e+00 | 0.0e+00 | 1229 | 74 | 20 | ACAT2,ACSS2,ACTG1,CTNNB1,CYP51A1,EBP,ETHE1,FDFT1,FDPS,HMGCR,HMGCS1,IDI1,LGALS3,LSS,NSDHL,S100A11,SC5D,SCD,STARD4,TP53INP1 |
| HALLMARK_MYOGENESIS | 0.0e+00 | 0.0e+00 | 1229 | 200 | 27 | ACSL1,APOD,APP,ATP6AP1,CHRNB1,COL6A2,DTNA,FDPS,FOXO4,GAA,GABARAPL2,HDAC5,ITGA7,ITGB1,LPIN1,MYL6B,MYO1C,NQO1,PC,PDE4DIP,PDLIM7,SCD,SIRT2,SORBS1,SVIL,TAGLN,TSC2 |
| HALLMARK_MITOTIC_SPINDLE | 0.0e+00 | 0.0e+00 | 1229 | 199 | 26 | ABI1,ABR,AKAP13,ARHGAP10,ARHGAP5,ARHGEF12,ARL8A,CAPZB,CDC42,CDC42EP2,CSNK1D,CYTH2,DST,DYNC1H1,KIF3C,KIFAP3,MARK4,NEDD9,NOTCH2,OPHN1,PALLD,RABGAP1,RASAL2,SPTBN1,STK38L,WASL |
| HALLMARK_ANDROGEN_RESPONSE | 0.0e+00 | 0.0e+00 | 1229 | 100 | 18 | ABHD2,APPBP2,ARID5B,DHCR24,HMGCR,HMGCS1,IDI1,INSIG1,ITGAV,MYL12A,NCOA4,PLPP1,PTPN21,SCD,SLC38A2,TMEM50A,ZBTB10,ZMIZ1 |
| HALLMARK_HEME_METABOLISM | 0.0e+00 | 0.0e+00 | 1229 | 200 | 23 | ALDH6A1,ARHGEF12,BLVRB,CLCN3,CTNS,CTSB,DMTN,FN3K,HTATIP2,KHNYN,LAMP2,LPIN2,LRP10,MBOAT2,MOSPD1,NCOA4,OPTN,PC,PGLS,PPP2R5B,SDCBP,SLC22A4,YPEL5 |
| HALLMARK_FATTY_ACID_METABOLISM | 0.0e+00 | 0.0e+00 | 1229 | 158 | 20 | ACAT2,ACOT8,ACOX1,ACSL1,DECR1,DHCR24,EHHADH,ERP29,GLUL,HADHB,HMGCS1,HSD17B11,IDH1,IDI1,INMT,NSDHL,RETSAT,SERINC1,TP53INP2,VNN1 |
| HALLMARK_APOPTOSIS | 0.0e+00 | 0.0e+00 | 1229 | 161 | 20 | APP,CTNNB1,CYLD,DCN,DNAJC3,EBP,HGF,HMOX1,IGF2R,IGFBP6,LGALS3,MADD,NEDD9,PPP2R5B,PSEN1,RETSAT,SC5D,SMAD7,SQSTM1,TIMP2 |
| HALLMARK_IL2_STAT5_SIGNALING | 0.0e+00 | 0.0e+00 | 1229 | 199 | 22 | AHNAK,ANXA4,CAPG,CD81,CDC42SE2,COL6A1,CYFIP1,FURIN,IGF2R,ITGAV,KLF6,MAP3K8,MAPKAPK2,MYO1C,PLPP1,RABGAP1L,SERPINB6,SMPDL3A,SNX14,SNX9,SWAP70,TWSG1 |
| HALLMARK_XENOBIOTIC_METABOLISM | 0.0e+00 | 0.0e+00 | 1229 | 200 | 22 | ACOX1,ADH5,AKR1C3,AQP9,BLVRB,CDA,DHRS7,HES6,HMOX1,HRG,HSD17B2,IDH1,LPIN2,NQO1,PC,PINK1,PMM1,PROS1,RETSAT,SLC12A4,UPB1,VNN1 |
| HALLMARK_APICAL_JUNCTION | 0.0e+00 | 1.0e-07 | 1229 | 200 | 21 | ACTG1,ARHGEF6,BAIAP2,CAP1,CD276,CERCAM,CTNNA1,EXOC4,GNAI2,INSIG1,ITGB1,MADCAM1,MDK,MPZL1,MSN,MYL12B,RRAS,SGCE,SIRPA,THBS3,WASL |
| HALLMARK_BILE_ACID_METABOLISM | 1.0e-07 | 5.0e-07 | 1229 | 112 | 15 | ABCA9,ACSL1,AQP9,ATXN1,CYP8B1,DHCR24,HSD17B11,IDH1,IDI1,OPTN,PAOX,PEX6,PHYH,PRDX5,RETSAT |
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION | 1.0e-07 | 6.0e-07 | 1229 | 200 | 20 | CALD1,CAPG,COL6A2,DAB2,DCN,DST,FAP,FBLN5,FZD8,ITGAV,ITGB1,LAMC1,LRP1,MATN3,NOTCH2,PLOD2,PMP22,SGCB,TAGLN,VIM |
| HALLMARK_PEROXISOME | 3.0e-07 | 1.1e-06 | 1229 | 104 | 14 | ACOT8,ACOX1,ACSL1,ATXN1,CLN8,DHCR24,EHHADH,FDPS,HSD17B11,IDH1,IDI1,PEX6,PRDX5,RETSAT |
| HALLMARK_COMPLEMENT | 6.0e-07 | 2.1e-06 | 1229 | 200 | 19 | APOC1,C1S,CDA,CP,CPQ,CTSB,CTSD,FCER1G,GNAI2,GNB2,LAMP2,LGALS3,LRP1,PCSK9,PRCP,PSEN1,RHOG,S100A13,TIMP2 |
| HALLMARK_MTORC1_SIGNALING | 6.0e-07 | 2.1e-06 | 1229 | 200 | 19 | ATP6V1D,CCNG1,CXCR4,CYP51A1,DHCR24,EBP,GSK3B,HMGCR,HMGCS1,IDH1,IDI1,INSIG1,PGM1,PLOD2,SC5D,SCD,SQSTM1,STARD4,TXNRD1 |
| HALLMARK_TGF_BETA_SIGNALING | 7.0e-07 | 2.2e-06 | 1229 | 54 | 10 | ACVR1,CTNNB1,FURIN,NCOR2,RAB31,RHOA,SKIL,SMAD7,SPTBN1,TGFBR1 |
| HALLMARK_UV_RESPONSE_DN | 3.0e-06 | 8.7e-06 | 1229 | 144 | 15 | ANXA4,ATP2B4,ATXN1,DAB2,FBLN5,INSIG1,LAMC1,MAP1B,NOTCH2,PMP22,PTPN21,SDC2,SMAD7,WDR37,ZMIZ1 |
| HALLMARK_WNT_BETA_CATENIN_SIGNALING | 7.3e-06 | 2.0e-05 | 1229 | 42 | 8 | ADAM17,CTNNB1,FRAT1,FZD8,HDAC5,NCOR2,NUMB,WNT5B |
| HALLMARK_COAGULATION | 8.5e-06 | 2.2e-05 | 1229 | 138 | 14 | APOC1,C1S,CPQ,CTSB,FURIN,GNB2,HRG,LAMP2,LRP1,MST1,PROS1,S100A13,SIRT2,USP11 |
| HALLMARK_HYPOXIA | 1.1e-05 | 2.5e-05 | 1229 | 200 | 17 | CAVIN3,CP,CXCR4,DCN,DTNA,EFNA1,FOSL2,GAA,HK1,HMOX1,KLF6,KLHL24,NAGK,PGM1,PRDX5,SDC2,SLC2A5 |
| HALLMARK_OXIDATIVE_PHOSPHORYLATION | 1.1e-05 | 2.5e-05 | 1229 | 200 | 17 | ACAT1,ALDH6A1,ATP6AP1,ATP6V0E1,ATP6V1C1,ATP6V1D,ATP6V1E1,COX6A1,COX6C,CYB5R3,DECR1,HADHA,HADHB,IDH1,PHYH,RETSAT,RHOT1 |
| HALLMARK_PROTEIN_SECRETION | 2.5e-05 | 5.6e-05 | 1229 | 96 | 11 | CD63,CLCN3,DST,GNAS,IGF2R,LAMP2,MAPK1,MON2,RAB9A,SNAP23,STX7 |
| HALLMARK_ADIPOGENESIS | 4.0e-05 | 8.0e-05 | 1229 | 200 | 16 | ACOX1,APLP2,CD151,COX6A1,DECR1,DHRS7,ESYT1,IDH1,ITGA7,PGM1,PHYH,RETSAT,RNF11,SORBS1,SPARCL1,TANK |
| HALLMARK_ESTROGEN_RESPONSE_EARLY | 4.0e-05 | 8.0e-05 | 1229 | 200 | 16 | ABHD2,BLVRB,DYNLT3,FAM102A,FDFT1,FRK,KDM4B,MED13L,NCOR2,NRIP1,RAB31,SH3BP5,SLC37A1,SNX24,SVIL,TTC39A |
| HALLMARK_P53_PATHWAY | 4.0e-05 | 8.0e-05 | 1229 | 200 | 16 | APP,BAIAP2,CCNG1,CD81,CTSD,CTSF,EPS8L2,FGF13,HMOX1,MXD4,PHLDA3,PMM1,RALGDS,RETSAT,RPS27L,SERTAD3 |
| HALLMARK_KRAS_SIGNALING_UP | 1.4e-04 | 2.7e-04 | 1229 | 200 | 15 | ADAM17,ADGRL4,APOD,CCSER2,CSF2RA,CXCR4,FCER1G,GALNT3,GPNMB,LY96,MTMR10,PTPRR,RABGAP1L,SPARCL1,ZNF277 |
| HALLMARK_PI3K_AKT_MTOR_SIGNALING | 2.7e-04 | 5.0e-04 | 1229 | 105 | 10 | ADCY2,ARPC3,CXCR4,DUSP3,GSK3B,ITPR2,MAPK1,SQSTM1,STAT2,TSC2 |
The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.
| gene_type | info |
|---|---|
| Dark Kinase (13) | ALPK3, CDC42BPB, CDK15, CDKL5, ICK, NEK10, NEK8, NRBP2, PAK3, PAK6, STK32C, STK36, WNK3 |
| Light Kinase (34) | ABL1, AXL, CKB, DGKA, DGKB, DMPK, EIF2AK4, EPHA1, EPHA5, ERBB2, FGR, IGF1R, IKBKB, IKBKE, LIMK2, LRRK2, MAP2K5, MAP3K11, MAP3K12, MAPK3, MYLK, NPR1, PIK3CB, PKDCC, PRKCD, PRKD1, PRKY, RAF1, ROS1, STK16, STRADA, TIE1, TRIO, ULK2 |
| Non-kinase Count | 1605 |
| label | pval | fdr | signature | geneset | overlap | hits |
|---|---|---|---|---|---|---|
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION | 0.0e+00 | 0.0e+00 | 1652 | 200 | 35 | ACTA2,ADAM12,ANPEP,BGN,BMP1,CADM1,CDH6,COL12A1,COL1A1,COL1A2,COL3A1,COL5A2,COL8A2,CXCL12,DKK1,EFEMP2,FBLN1,FBLN2,FSTL1,GAS1,LAMA3,MGP,MMP2,MYL9,MYLK,PCOLCE,PCOLCE2,PMEPA1,SNTB1,SPARC,TGFBI,TGFBR3,TPM1,TPM4,WNT5A |
| HALLMARK_ESTROGEN_RESPONSE_EARLY | 0.0e+00 | 0.0e+00 | 1652 | 200 | 35 | AKAP1,ALDH3B1,AR,ASB13,B4GALT1,CA12,CALCR,CCN5,CELSR1,CISH,CLDN7,CLIC3,CXCL12,ELOVL5,ESRP2,FKBP5,GFRA1,GREB1,IGF1R,KCNK15,MINDY1,MYOF,NAV2,OLFML3,OPN3,PDZK1,PEX11A,SEMA3B,SLC1A1,SLC22A5,SLC26A2,SLC27A2,SYT12,TMEM164,TSKU |
| HALLMARK_ADIPOGENESIS | 0.0e+00 | 0.0e+00 | 1652 | 200 | 33 | ACADL,ACADS,ACLY,ADCY6,ANGPT1,APOE,C3,CAVIN2,CD36,COL15A1,COQ9,CPT2,CYP4B1,DBT,DNAJC15,ETFB,GPAM,HADH,ITSN1,JAGN1,MARC2,MCCC1,MYLK,ORM1,PDCD4,PHLDB1,PPM1B,SCP2,SDHC,SLC25A1,SULT1A1,UCP2,VEGFB |
| HALLMARK_ESTROGEN_RESPONSE_LATE | 0.0e+00 | 0.0e+00 | 1652 | 200 | 31 | ALDH3B1,ASCL1,CA12,CALCR,CCN5,CISH,CKB,CLIC3,CPE,CXCL12,DLG5,ELOVL5,ETFB,FKBP5,GPER1,IMPA2,MYOF,OPN3,PDCD4,PDZK1,PLXNB1,SEMA3B,SERPINA3,SERPINA5,SLC22A5,SLC26A2,SLC27A2,SLC2A8,ST6GALNAC2,TNNC1,TRIM29 |
| HALLMARK_MYOGENESIS | 0.0e+00 | 0.0e+00 | 1652 | 200 | 28 | ADAM12,AGL,AK1,ANKRD2,CASQ1,CAV3,CD36,CKB,COL15A1,COL1A1,COL3A1,DMPK,EFS,ENO3,ITGB4,LDB3,MB,MRAS,MYLK,MYOM1,NAV2,PLXNB2,PSEN2,PYGM,SPARC,TNNC1,TNNI2,VIPR1 |
| HALLMARK_P53_PATHWAY | 0.0e+00 | 0.0e+00 | 1652 | 200 | 28 | ABHD4,ADA,AK1,ALOX15B,BLCAP,BTG2,CCND3,CDKN2B,CLCA2,DGKA,ERCC5,F2R,HEXIM1,ITGB4,PLXNB2,RXRA,SESN1,SLC35D1,STEAP3,TAX1BP3,TCHH,TCN2,TP53,TP63,TSPYL2,VAMP8,VDR,ZBTB16 |
| HALLMARK_FATTY_ACID_METABOLISM | 0.0e+00 | 0.0e+00 | 1652 | 158 | 24 | ACADL,ACADS,ACOT2,ALDH3A1,ALDH9A1,AOC3,AQP7,AUH,CD36,CEL,CPOX,CPT2,ECI2,ELOVL5,ENO3,FMO1,GPD1,HADH,HPGD,MAOA,RDH11,SDHC,SLC22A5,SUCLG2 |
| HALLMARK_APICAL_JUNCTION | 0.0e+00 | 0.0e+00 | 1652 | 200 | 26 | ACTG2,ACTN1,ACTN4,ALOX15B,B4GALT1,BMP1,CADM3,CDH6,CLDN7,CNN2,FSCN1,GNAI1,GRB7,HADH,INPPL1,ITGB4,LAMA3,LIMA1,MMP2,MYL9,NLGN3,PIK3CB,PIK3R3,PTPRC,TGFBI,VWF |
| HALLMARK_UV_RESPONSE_DN | 0.0e+00 | 1.0e-07 | 1652 | 144 | 21 | AGGF1,APBB2,ATRN,COL1A1,COL1A2,COL3A1,COL5A2,DMAC2L,EFEMP1,ERBB2,IGF1R,IGFBP5,MAP2K5,MIOS,NFIB,PIAS3,PIK3R3,RBPMS,RXRA,SMAD3,TGFBR3 |
| HALLMARK_XENOBIOTIC_METABOLISM | 0.0e+00 | 1.0e-07 | 1652 | 200 | 25 | ABCC3,ALDH3A1,ALDH9A1,APOE,ATOH8,BCAR1,CD36,CFB,CRP,CYP17A1,CYP2C18,CYP2E1,DHRS1,ELOVL5,ENTPD5,FBLN1,FMO1,FMO3,IL1R1,MAOA,PPARD,PTGDS,SERPINA6,SLC35D1,SLC46A3 |
| HALLMARK_BILE_ACID_METABOLISM | 2.0e-07 | 8.0e-07 | 1652 | 112 | 17 | ABCA4,ABCA8,ABCD1,ALDH9A1,AR,CYP7B1,HSD3B7,NUDT12,PEX11A,PEX11G,PEX13,PXMP2,RXRA,SCP2,SERPINA6,SLC27A2,SULT1B1 |
| HALLMARK_PEROXISOME | 3.0e-07 | 1.3e-06 | 1652 | 104 | 16 | ABCD1,ALDH9A1,CADM1,CEL,ECI2,ELOVL5,HSD3B7,PEX11A,PEX11B,PEX13,RDH11,SCP2,SEMA3C,SERPINA6,SLC27A2,STS |
| HALLMARK_COMPLEMENT | 3.5e-06 | 1.3e-05 | 1652 | 200 | 21 | APOBEC3G,C1R,C3,CALM3,CD36,CFB,CR1,CTSH,CTSO,CTSS,DPP4,GATA3,GMFB,KCNIP3,MMP12,MSRB1,OLR1,PLSCR1,PRKCD,PRSS36,RAF1 |
| HALLMARK_HEME_METABOLISM | 1.2e-05 | 4.4e-05 | 1652 | 200 | 20 | ACKR1,AGPAT4,ALDH1L1,BTG2,C3,CCND3,CPOX,ELL2,FBXO9,KAT2B,NFE2,NNT,PDZK1IP1,PIGQ,RHAG,SELENBP1,SIDT2,TAL1,TMEM9B,UCP2 |
| HALLMARK_COAGULATION | 5.6e-05 | 1.9e-04 | 1652 | 138 | 15 | APOC3,BMP1,C1R,C3,CFB,CRIP2,CTSH,CTSO,DPP4,MMP2,MMP7,MSRB2,OLR1,SPARC,VWF |
| HALLMARK_APICAL_SURFACE | 8.6e-05 | 2.7e-04 | 1652 | 44 | 8 | ATP6V0A4,B4GALT1,EFNA5,FLOT2,GAS1,GATA3,PKHD1,RTN4RL1 |
The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.
| gene_type | info |
|---|---|
| Dark Kinase (12) | BRSK1, CDK11B, CDK16, CSNK1G3, MAP3K21, MARK3, PHKG1, RIOK1, RIOK2, RPS6KL1, STK40, VRK2 |
| Light Kinase (35) | AURKA, CASK, CDK4, CDK8, CSNK1A1, CSNK2A1, DGKG, EIF2AK2, EPHA2, FLT1, GAK, HK2, HUNK, IRAK2, MAP2K1, MAP3K4, MAPK9, MAPKAPK3, MAPKAPK5, MARK2, PAK4, PDPK2P, PIM1, PIM2, PLK2, PLK3, PRKAA1, RPS6KB1, SGK3, TAF1, TBK1, TEX14, TRIB2, TRIB3, TRIM33 |
| Non-kinase Count | 1556 |
| label | pval | fdr | signature | geneset | overlap | hits |
|---|---|---|---|---|---|---|
| HALLMARK_MYC_TARGETS_V1 | 0.0e+00 | 0.0e+00 | 1603 | 200 | 68 | ABCE1,ACP1,CANX,CBX3,CCT2,CCT3,CCT4,CCT5,CCT7,CDK4,CNBP,COPS5,DDX18,DDX21,EIF2S1,EIF2S2,EIF3D,EIF3J,EIF4H,EPRS1,ETF1,G3BP1,GLO1,GNL3,HSP90AB1,IARS1,ILF2,KARS1,MYC,NOLC1,NPM1,ODC1,PABPC4,POLD2,PRDX4,PSMA4,PSMA6,PSMB3,PSMD14,PSMD3,PSMD7,RACK1,RAD23B,RPL14,RPL18,RPL34,RPL6,RPLP0,RPS10,RPS2,RPS3,RPS5,RPS6,RSL1D1,RUVBL2,SF3A1,SNRPB2,SRSF1,SRSF3,SRSF7,TARDBP,TCP1,TUFM,U2AF1,XPO1,XPOT,XRCC6,YWHAE |
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE | 0.0e+00 | 0.0e+00 | 1603 | 113 | 32 | ALDH18A1,ASNS,ATF3,BANF1,CEBPG,CHAC1,CXXC1,DDX10,DNAJB9,EIF2S1,EIF4EBP1,EXOSC1,FKBP14,GOSR2,HERPUD1,IARS1,MTHFD2,MTREX,NFYA,NOLC1,NOP14,NPM1,PDIA6,PSAT1,RPS14,SDAD1,SERP1,SLC7A5,SRPRA,STC2,TARS1,XPOT |
| HALLMARK_MTORC1_SIGNALING | 0.0e+00 | 0.0e+00 | 1603 | 200 | 40 | ARPC5L,ASNS,AURKA,BCAT1,CANX,CCT6A,CFP,COPS5,CTH,DDIT3,DDX39A,EIF2S2,EPRS1,ETF1,GCLC,HK2,HSPA4,IMMT,M6PR,MTHFD2,NAMPT,NMT1,PHGDH,PNO1,PNP,PSAT1,PSMA4,PSMD13,PSMD14,PSMG1,RPN1,SERP1,SHMT2,SLC1A5,SLC7A5,TBK1,TCEA1,TFRC,TRIB3,UFM1 |
| HALLMARK_TNFA_SIGNALING_VIA_NFKB | 0.0e+00 | 0.0e+00 | 1603 | 200 | 36 | AREG,ATF3,BTG3,CCL20,CCL5,CD44,CXCL2,CXCL3,DUSP2,DUSP4,DUSP5,EIF1,FOSB,FOSL1,GADD45A,GFPT2,HBEGF,HES1,IER2,IER5,IFNGR2,IL15RA,IL23A,KLF10,MAFF,MCL1,MYC,NAMPT,PANX1,PHLDA1,PLK2,SLC16A6,SPHK1,TLR2,TNC,ZFP36 |
| HALLMARK_MYC_TARGETS_V2 | 0.0e+00 | 0.0e+00 | 1603 | 58 | 17 | BYSL,CBX3,CDK4,DDX18,DUSP2,GNL3,HK2,IMP4,MYC,NDUFAF4,NOLC1,NOP2,NPM1,RABEPK,RRP12,TFB2M,WDR43 |
| HALLMARK_G2M_CHECKPOINT | 0.0e+00 | 0.0e+00 | 1603 | 200 | 26 | AURKA,CDK4,DDX39A,EZH2,G3BP1,H2BC12,HMGA1,HUS1,KATNA1,LIG3,MNAT1,MT2A,MYC,NOLC1,NUP98,ODC1,PAFAH1B1,PRIM2,PRMT5,RAD23B,SLC7A1,SLC7A5,SRSF1,UPF1,WRN,XPO1 |
| HALLMARK_E2F_TARGETS | 0.0e+00 | 2.0e-07 | 1603 | 200 | 24 | AK2,ASF1A,AURKA,CDK4,DDX39A,EIF2S1,EZH2,HMGA1,HUS1,MTHFD2,MYC,NBN,NOLC1,POLD2,POLE4,PPM1D,PRDX4,PRIM2,SRSF1,TFRC,TIPIN,XPO1,XRCC6,ZW10 |
| HALLMARK_P53_PATHWAY | 0.0e+00 | 2.0e-07 | 1603 | 200 | 24 | AEN,ATF3,DDIT3,EPHA2,FAS,GADD45A,HBEGF,IER5,MAPKAPK3,OSGIN1,PDGFA,PLK2,PLK3,PPM1D,RACK1,RAD9A,RPL18,RPL36,RPS12,SEC61A1,SERPINB5,SPHK1,TGFA,TRIB3 |
| HALLMARK_UV_RESPONSE_UP | 0.0e+00 | 2.0e-07 | 1603 | 158 | 21 | ASNS,ATF3,BTG3,CDC34,CEBPG,CXCL2,DDX21,EIF2S3,FOSB,HSPA13,HTR7,MARK2,MSX1,NUP58,POLR2H,PRPF3,RAB27A,RPN1,TARS1,TFRC,TMBIM6 |
| HALLMARK_ANDROGEN_RESPONSE | 1.0e-07 | 6.0e-07 | 1603 | 100 | 16 | ABCC4,ADAMTS1,CENPN,DNAJB9,ELK4,GNAI3,HOMER2,HSD17B14,LMAN1,NGLY1,PGM3,RRP12,SEC24D,SMS,UAP1,XRCC6 |
| HALLMARK_ALLOGRAFT_REJECTION | 2.2e-06 | 9.1e-06 | 1603 | 200 | 21 | AARS1,ABCE1,BCAT1,BCL10,CCL5,CFP,DARS1,EIF3D,EIF3J,EREG,FAS,HLA-A,IFNGR2,IL4R,NPM1,RPL39,RPL9,RPS19,RPS3A,RPS9,TLR2 |
| HALLMARK_INFLAMMATORY_RESPONSE | 2.2e-06 | 9.1e-06 | 1603 | 200 | 21 | ADORA2B,CCL20,CCL5,CD14,EIF2AK2,EREG,GNAI3,HBEGF,HRH1,IFNGR2,IL15RA,IL4R,IRAK2,MYC,NAMPT,SELENOS,SLC1A2,SLC31A1,SLC7A1,SPHK1,TLR2 |
| HALLMARK_GLYCOLYSIS | 7.9e-06 | 2.8e-05 | 1603 | 200 | 20 | ADORA2B,AURKA,CD44,COPB2,CTH,ECD,GCLC,GFPT1,GMPPA,GNPDA1,HAX1,HK2,PFKP,PGAM1,PMM2,QSOX1,SLC35A3,STC2,TGFA,TXN |
| HALLMARK_KRAS_SIGNALING_UP | 7.9e-06 | 2.8e-05 | 1603 | 200 | 20 | BPGM,CCL20,CD37,DNMBP,DUSP6,EMP1,EREG,ETV4,ETV5,GFPT2,HBEGF,MALL,PLEK2,PRELID3B,PTBP2,SNAP25,SPRY2,TRIB2,USP12,WDR33 |
| HALLMARK_APOPTOSIS | 1.8e-05 | 6.1e-05 | 1603 | 161 | 17 | ANXA1,ATF3,BCL10,BTG3,CD14,CD44,CTH,DAP3,DDIT3,DFFA,EMP1,EREG,ETF1,FAS,GADD45A,MCL1,PMAIP1 |
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY | 2.3e-05 | 7.1e-05 | 1603 | 49 | 9 | GCLC,GCLM,GLRX2,PFKP,PRDX4,PRNP,SELENOS,SRXN1,TXN |
| HALLMARK_IL2_STAT5_SIGNALING | 2.5e-05 | 7.4e-05 | 1603 | 199 | 19 | BATF3,CD44,EMP1,ETV4,HK2,IL4R,MAFF,MYC,NOP2,ODC1,PHLDA1,PIM1,PNP,PRNP,PTRH2,SLC1A5,SPRED2,SPRY4,ST3GAL4 |
| HALLMARK_INTERFERON_GAMMA_RESPONSE | 2.7e-05 | 7.5e-05 | 1603 | 200 | 19 | BPGM,CCL5,EIF2AK2,FAS,GBP6,HLA-A,IL15RA,IL18BP,IL4R,LAP3,MT2A,MTHFD2,NAMPT,NUP93,P2RY14,PFKP,PIM1,PNP,RAPGEF6 |
| HALLMARK_ESTROGEN_RESPONSE_EARLY | 8.8e-05 | 2.3e-04 | 1603 | 200 | 18 | AREG,CANT1,CD44,FHL2,HES1,KLF10,MREG,MYC,NBL1,PMAIP1,RRP12,SIAH2,SLC16A1,SLC39A6,SLC7A5,STC2,TFAP2C,THSD4 |
| HALLMARK_IL6_JAK_STAT3_SIGNALING | 1.1e-04 | 2.7e-04 | 1603 | 87 | 11 | CD14,CD44,CXCL3,FAS,HAX1,IFNGR2,IL15RA,IL4R,INHBE,PIM1,TLR2 |
| HALLMARK_PROTEIN_SECRETION | 2.6e-04 | 6.1e-04 | 1603 | 96 | 11 | ARFGAP3,COPB1,COPB2,COPE,GOLGA4,GOSR2,LMAN1,M6PR,RAB2A,SEC24D,ZW10 |
| HALLMARK_XENOBIOTIC_METABOLISM | 2.7e-04 | 6.1e-04 | 1603 | 200 | 17 | ACP1,AP4B1,BCAT1,EPHA2,FAS,GCLC,HACL1,KARS1,LEAP2,LONP1,MT2A,NMT1,PYCR1,SHMT2,SLC1A5,TMBIM6,TYR |
The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.
| gene_type | info |
|---|---|
| Dark Kinase (11) | ADCK1, ADCK5, CDC42BPG, COQ8B, CSNK2A3, MAST3, NEK9, PRAG1, PRKACB, STK32A, TAOK2 |
| Light Kinase (31) | BCR, BRD3, CKMT1A, CKMT1B, DGKQ, EIF2AK1, EPHA7, EPHB6, ERBB3, ERBB4, KDR, LIMK1, MAP3K13, MAP3K5, MAP4K2, MINK1, PRKACA, PRKCA, PRKCH, PRKX, PTK2B, ROCK2, RPS6KA2, RPS6KA6, SGK1, STK11, STK38, TGFBR2, TNK2, TRIM66, UHMK1 |
| Non-kinase Count | 1458 |
| label | pval | fdr | signature | geneset | overlap | hits |
|---|---|---|---|---|---|---|
| HALLMARK_OXIDATIVE_PHOSPHORYLATION | 0.0e+00 | 0.0e+00 | 1500 | 200 | 27 | ACADSB,ATP5F1C,ATP5F1D,ATP5F1E,ATP5PD,COX7A2,COX7C,CYB5A,ETFDH,GPX4,IDH2,MAOB,MPC1,NDUFB1,NDUFB3,NDUFB5,OGDH,OXA1L,PDHB,SLC25A11,SLC25A12,SLC25A20,SURF1,TIMM8B,UQCR11,UQCRB,UQCRQ |
| HALLMARK_GLYCOLYSIS | 0.0e+00 | 1.0e-07 | 1500 | 200 | 25 | AGRN,ALDH7A1,ALG1,ARPP19,B3GALT6,B3GAT3,BPNT1,CHST12,CHST2,CLDN9,COG2,CYB5A,GALK1,GLCE,HOMER1,LHPP,NDST3,PKP2,PPIA,PYGB,SDC3,SLC16A3,SRD5A3,STC1,XYLT2 |
| HALLMARK_ESTROGEN_RESPONSE_LATE | 0.0e+00 | 7.0e-07 | 1500 | 200 | 23 | ABCA3,AGR2,ALDH3A2,ARL3,CD9,CELSR2,DCXR,HR,IDH2,ITPK1,LLGL2,NAB2,PLAAT3,RPS6KA2,SCARB1,SCNN1A,SGK1,SLC9A3R1,SNX10,TIAM1,TPD52L1,TST,UNC13B |
| HALLMARK_ADIPOGENESIS | 8.0e-07 | 7.7e-06 | 1500 | 200 | 21 | ABCB8,ADIPOQ,CAVIN1,COL4A1,COQ5,CRAT,DGAT1,ELOVL6,FZD4,GPHN,GPX4,LIFR,LIPE,LPCAT3,LPL,REEP6,SCARB1,SLC66A3,TST,UQCR11,UQCRQ |
| HALLMARK_APICAL_JUNCTION | 8.0e-07 | 7.7e-06 | 1500 | 200 | 21 | CDH8,CLDN11,CLDN9,CRAT,EVL,IRS1,ITGA3,JUP,LDLRAP1,MAP4K2,MYH10,NRTN,PECAM1,PTEN,RSU1,SDC3,SKAP2,TAOK2,TMEM8B,VCL,YWHAH |
| HALLMARK_PEROXISOME | 2.9e-06 | 2.1e-05 | 1500 | 104 | 14 | ABCD2,ABCD3,CRAT,DLG4,GSTK1,HMGCL,IDH2,ITGB1BP1,MLYCD,MVP,PEX2,PEX5,SLC35B2,YWHAH |
| HALLMARK_HEME_METABOLISM | 3.0e-06 | 2.1e-05 | 1500 | 200 | 20 | ARL2BP,ATP6V0A1,EIF2AK1,EPOR,ERMAP,GDE1,H1-0,LMO2,MARCHF2,MINPP1,PPOX,RNF123,SEC14L1,SLC10A3,SLC2A1,SNCA,TENT5C,TRAK2,TRIM58,UROS |
| HALLMARK_BILE_ACID_METABOLISM | 7.0e-06 | 4.4e-05 | 1500 | 112 | 14 | ABCA3,ABCD2,ABCD3,AMACR,CROT,GSTK1,IDH2,LIPE,MLYCD,NR1H4,PEX1,PEX7,SLC22A18,SLC35B2 |
| HALLMARK_P53_PATHWAY | 1.1e-05 | 6.1e-05 | 1500 | 200 | 19 | CDKN1A,DCXR,GM2A,H1-2,H2AJ,H2AW,IFI30,JAG2,PITPNC1,PRMT2,PTPN14,RAP2B,S100A4,TGFB1,TM7SF3,TPD52L1,XPC,ZMAT3,ZNF365 |
| HALLMARK_COAGULATION | 1.9e-05 | 9.3e-05 | 1500 | 138 | 15 | CASP9,CD9,CFI,CSRP1,DUSP14,F2RL2,F8,FN1,GNG12,HTRA1,PECAM1,PREP,RABIF,SERPING1,TF |
| HALLMARK_UV_RESPONSE_DN | 3.1e-05 | 1.4e-04 | 1500 | 144 | 15 | ANXA2,BCKDHB,CDON,DBP,DDAH1,GJA1,ID1,IRS1,LPAR1,MT1E,PRKCA,PTEN,PTPRM,SLC22A18,TGFBR2 |
| HALLMARK_ESTROGEN_RESPONSE_EARLY | 3.8e-05 | 1.5e-04 | 1500 | 200 | 18 | ABCA3,ABLIM1,ADCY1,ADCY9,ARL3,BCL11B,CELSR2,GJA1,HR,ITPK1,PLAAT3,RPS6KA2,SCARB1,SCNN1A,SLC2A1,SLC9A3R1,TIAM1,TPD52L1 |
| HALLMARK_XENOBIOTIC_METABOLISM | 3.8e-05 | 1.5e-04 | 1500 | 200 | 18 | ABCD2,ACP2,ARPP19,BPHL,CROT,CSAD,CYB5A,DCXR,ENPEP,ESR1,ETFDH,G6PC,JUP,MAN1A1,MPP2,SERTAD1,SPINT2,TKFC |
| HALLMARK_FATTY_ACID_METABOLISM | 9.0e-05 | 3.2e-04 | 1500 | 158 | 15 | ALDH3A2,BCKDHB,BPHL,CRAT,ETFDH,GSTZ1,HMGCL,LGALS1,MLYCD,PDHB,PPARA,REEP6,UBE2L6,UROS,YWHAH |
| HALLMARK_DNA_REPAIR | 1.8e-04 | 6.1e-04 | 1500 | 150 | 14 | APRT,DAD1,ERCC2,ERCC4,GPX4,MPG,POLR2E,POLR3GL,RBX1,SUPT4H1,SURF1,TAF10,TSG101,XPC |
The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.
| gene_type | info |
|---|---|
| Dark Kinase (9) | ALPK2, BRSK2, CDK18, CDKL2, LTK, MAP3K14, PXK, STK31, STK33 |
| Light Kinase (19) | ACVR1B, AKT3, BRDT, DAPK3, EPHA4, ERN1, FES, FYN, GRK5, LCK, MAK, MAP3K9, MAP4K5, MERTK, NPR2, PRKCE, PRKG1, TNK1, TNNI3K |
| Non-kinase Count | 962 |
| label | pval | fdr | signature | geneset | overlap | hits |
|---|---|---|---|---|---|---|
| HALLMARK_GLYCOLYSIS | 0.0e+00 | 0.0e+00 | 990 | 200 | 22 | ARTN,CAPN5,CHPF2,CHST1,CITED2,COL5A1,FUT8,G6PD,GOT1,HS2ST1,HSPA5,KDELR3,LHX9,ME2,MERTK,P4HA1,P4HA2,PAM,PGM2,SOX9,UGP2,VLDLR |
| HALLMARK_HYPOXIA | 1.0e-07 | 3.0e-06 | 990 | 200 | 18 | CITED2,COL5A1,EDN2,FOXO3,HSPA5,KDELR3,LOX,P4HA1,P4HA2,PAM,PGM2,PPARGC1A,STBD1,TMEM45A,TPST2,UGP2,VLDLR,XPNPEP1 |
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION | 6.0e-07 | 1.0e-05 | 990 | 200 | 17 | APLP1,COL5A1,CXCL8,ECM2,FBN1,FLNA,FUCA1,ID2,IL15,LOX,LUM,MAGEE1,MATN2,NID2,OXTR,P3H1,RHOB |
| HALLMARK_ADIPOGENESIS | 1.2e-05 | 1.6e-04 | 990 | 200 | 15 | ACAA2,ARL4A,ECH1,ENPP2,EPHX2,FABP4,FAH,MGST3,PPP1R15B,PREB,SLC27A1,SSPN,STOM,TOB1,YWHAG |
| HALLMARK_ESTROGEN_RESPONSE_EARLY | 5.1e-05 | 3.7e-04 | 990 | 200 | 14 | ABAT,AQP3,FLNB,KRT8,LRIG1,MAPT,P2RY2,PRSS23,RETREG1,SYNGR1,TJP3,TOB1,TUBB2B,WFS1 |
| HALLMARK_KRAS_SIGNALING_DN | 5.1e-05 | 3.7e-04 | 990 | 200 | 14 | BRDT,EDN2,KCNE2,LYPD3,MFSD6,MX1,MYOT,P2RY4,PDE6B,RYR2,SNN,TFF2,THNSL2,THRB |
| HALLMARK_P53_PATHWAY | 5.1e-05 | 3.7e-04 | 990 | 200 | 14 | ABAT,ACVR1B,BAK1,CGRRF1,EPHX1,FOXO3,FUCA1,PERP,PROCR,STOM,TNNI1,TOB1,TSC22D1,VWA5A |
| HALLMARK_UV_RESPONSE_UP | 8.0e-05 | 5.0e-04 | 990 | 158 | 12 | AQP3,ATP6V1F,BAK1,BSG,C4BPB,CREG1,EPHX1,NAT1,NPTXR,PLCL1,RHOB,YKT6 |
| HALLMARK_COAGULATION | 1.0e-04 | 5.7e-04 | 990 | 138 | 11 | ADAM9,CAPN5,CTSK,FBN1,FYN,GSN,MMP11,MMP15,PLG,PRSS23,RAPGEF3 |
The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.
| gene_type | info |
|---|---|
| Dark Kinase (8) | ADCK2, CAMKK2, CDK13, CSNK1G2, MAST4, NEK6, SCYL3, TP53RK |
| Light Kinase (16) | ALPK1, CLK2, EGFR, MTOR, NLK, PDGFRA, PDK4, PIK3CG, PKN1, PKN2, ROR1, RYK, STK24, STK39, TBRG4, TEK |
| Non-kinase Count | 876 |
| label | pval | fdr | signature | geneset | overlap | hits |
|---|---|---|---|---|---|---|
| HALLMARK_KRAS_SIGNALING_UP | 0.0e+00 | 0.0e+00 | 900 | 200 | 20 | ALDH1A3,BIRC3,BTBD3,CA2,ETV1,FBXO4,GNG11,ITGBL1,LAPTM5,LAT2,LIF,MPZL2,PDCD1LG2,PLAU,PRRX1,PSMB8,RELN,RGS16,SCG5,TMEM158 |
| HALLMARK_OXIDATIVE_PHOSPHORYLATION | 0.0e+00 | 1.0e-07 | 900 | 200 | 19 | AIFM1,ATP5F1A,ATP5MC1,ATP5MC2,ATP5ME,ATP5PO,COX17,COX8A,FH,ISCU,MDH2,MRPS11,MTX2,NDUFA7,NDUFB6,NDUFS1,NDUFV1,PDK4,UQCRFS1 |
| HALLMARK_DNA_REPAIR | 6.0e-07 | 1.1e-05 | 900 | 150 | 14 | CCNO,COX17,DDB2,ERCC1,GSDME,IMPDH2,MRPL40,NCBP2,NELFB,NELFE,POLR2G,POLR2I,SAC3D1,TAF9 |
| HALLMARK_INTERFERON_ALPHA_RESPONSE | 1.0e-05 | 1.3e-04 | 900 | 97 | 10 | BATF2,CASP1,CMTR1,IFI44L,IFITM1,IRF2,MVB12A,PSMB8,PSMB9,TAP1 |
| HALLMARK_XENOBIOTIC_METABOLISM | 1.8e-05 | 1.8e-04 | 900 | 200 | 14 | AHCY,ASL,CA2,CES1,CNDP2,DHPS,GCH1,GSS,IGFBP4,NINJ1,PDK4,PEMT,PSMB10,XDH |
| HALLMARK_FATTY_ACID_METABOLISM | 3.2e-05 | 2.6e-04 | 900 | 158 | 12 | ACSL4,ACSL5,ADSL,ALDH1A1,CA2,CYP4A11,FH,GCDH,GRHPR,MDH2,MGLL,PTPRG |
| HALLMARK_BILE_ACID_METABOLISM | 3.7e-05 | 2.6e-04 | 900 | 112 | 10 | ABCA6,ACSL5,ALDH1A1,EFHC1,GNPAT,LONP2,NEDD4,NR3C2,PEX12,SLC27A5 |
| HALLMARK_IL2_STAT5_SIGNALING | 7.3e-05 | 3.5e-04 | 900 | 199 | 13 | AHCY,CA2,CCR4,IKZF2,IL18R1,IL1RL1,LIF,MUC1,NCS1,PDCD2L,RGS16,SYNGR2,UCK2 |
| HALLMARK_ADIPOGENESIS | 7.7e-05 | 3.5e-04 | 900 | 200 | 13 | AIFM1,ATP5PO,COQ3,COX8A,ESRRA,MDH2,MGLL,MRAP,MTCH2,PEMT,QDPR,RMDN3,SQOR |
| HALLMARK_INFLAMMATORY_RESPONSE | 7.7e-05 | 3.5e-04 | 900 | 200 | 13 | CD82,GCH1,HAS2,IFITM1,IL18R1,LIF,MARCO,MEFV,RGS16,SGMS2,SRI,TLR3,TPBG |
| HALLMARK_INTERFERON_GAMMA_RESPONSE | 7.7e-05 | 3.5e-04 | 900 | 200 | 13 | BATF2,CASP1,CMTR1,GCH1,IFI44L,IRF2,NLRC5,PSMB10,PSMB8,PSMB9,SRI,TAP1,VCAM1 |
The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.
| gene_type | info |
|---|---|
| Dark Kinase (6) | CDK20, CLK4, DYRK3, DYRK4, NEK3, NUAK2 |
| Light Kinase (12) | ACVR2B, AURKC, BMPR1B, BRAF, CDK7, CSNK1E, MAP3K20, PIM3, PTK6, RIPK2, TRIB1, TRPM6 |
| Non-kinase Count | 536 |
| label | pval | fdr | signature | geneset | overlap | hits |
|---|---|---|---|---|---|---|
| HALLMARK_TNFA_SIGNALING_VIA_NFKB | 0.0e+00 | 0.0e+00 | 554 | 200 | 50 | BHLHE40,BIRC2,BMP2,BTG1,CEBPB,CFLAR,CSF2,CXCL1,CXCL10,DDX58,DRAM1,ETS2,GADD45B,ICAM1,IFIH1,IFIT2,IL1A,IL1B,IL6,INHBA,IRF1,JAG1,KYNU,LAMB3,MSC,NFKB2,NFKBIA,NFKBIE,PER1,PHLDA2,PLAUR,PLEK,PNRC1,PTGS2,PTX3,RELB,RIPK2,SERPINB8,SOD2,SPSB1,STAT5A,TGIF1,TNFAIP2,TNFAIP3,TNFAIP8,TNIP1,TRAF1,TRIB1,VEGFA,ZC3H12A |
| HALLMARK_INTERFERON_GAMMA_RESPONSE | 0.0e+00 | 0.0e+00 | 554 | 200 | 27 | BTG1,CMPK2,CXCL10,DDX58,DHX58,GBP4,ICAM1,IDO1,IFIH1,IFIT1,IFIT2,IL6,IRF1,ISG15,NFKBIA,PARP12,PTGS2,RBCK1,RIPK2,RSAD2,SOCS1,SOD2,TNFAIP2,TNFAIP3,TXNIP,UPP1,WARS1 |
| HALLMARK_KRAS_SIGNALING_UP | 0.0e+00 | 0.0e+00 | 554 | 200 | 21 | AVL9,BMP2,C3AR1,CSF2,CXCL10,ETS1,HDAC9,HSD11B1,IKZF1,IL1B,INHBA,NGF,PLAUR,PRDM1,PTGS2,RBM4,ST6GAL1,TNFAIP3,TRAF1,TRIB1,TSPAN1 |
| HALLMARK_INTERFERON_ALPHA_RESPONSE | 0.0e+00 | 0.0e+00 | 554 | 97 | 15 | CMPK2,CXCL10,DHX58,GBP4,HLA-C,IFIH1,IFIT2,IRF1,ISG15,NUB1,PARP12,RIPK2,RSAD2,TXNIP,WARS1 |
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION | 0.0e+00 | 0.0e+00 | 554 | 200 | 18 | CXCL1,FERMT2,FGF2,GADD45B,IL32,IL6,INHBA,LAMC2,MMP1,PDLIM4,PLAUR,PPIB,PTX3,SNAI2,TFPI2,TNFAIP3,TNFRSF12A,VEGFA |
| HALLMARK_INFLAMMATORY_RESPONSE | 0.0e+00 | 0.0e+00 | 554 | 200 | 18 | C3AR1,CSF3,CSF3R,CXCL10,GNA15,ICAM1,IL1A,IL1B,IL6,INHBA,IRF1,NFKBIA,NLRP3,PLAUR,RIPK2,RNF144B,SLC11A2,SLC7A2 |
| HALLMARK_HYPOXIA | 0.0e+00 | 1.0e-07 | 554 | 200 | 15 | AMPD3,BHLHE40,BTG1,CCNG2,CDKN1B,DDIT4,ETS1,GCNT2,HOXB9,IL6,NR3C1,PLAUR,PNRC1,TNFAIP3,VEGFA |
| HALLMARK_APOPTOSIS | 0.0e+00 | 2.0e-07 | 554 | 161 | 13 | BMP2,CDKN1B,CFLAR,GADD45B,GNA15,IL1A,IL1B,IL6,IRF1,KRT18,SOD2,TNFRSF12A,TXNIP |
| HALLMARK_IL6_JAK_STAT3_SIGNALING | 0.0e+00 | 3.0e-07 | 554 | 87 | 10 | CSF2,CSF3R,CXCL1,CXCL10,IL1B,IL6,IRF1,LTBR,SOCS1,TNFRSF12A |
| HALLMARK_ALLOGRAFT_REJECTION | 1.0e-07 | 3.0e-07 | 554 | 200 | 14 | DYRK3,ELF4,ETS1,HCLS1,HDAC9,ICAM1,IL1B,IL6,INHBA,NCK1,NLRP3,RIPK2,SOCS1,WARS1 |
| HALLMARK_IL2_STAT5_SIGNALING | 2.7e-06 | 1.2e-05 | 554 | 199 | 12 | BHLHE40,BMP2,CDCP1,CSF2,CXCL10,GADD45B,GBP4,GSTO1,NFKBIZ,SOCS1,TRAF1,XBP1 |
| HALLMARK_P53_PATHWAY | 2.8e-06 | 1.2e-05 | 554 | 200 | 12 | BMP2,BTG1,CDH13,DDIT4,DRAM1,IL1A,KRT17,NUPR1,SOCS1,TXNIP,UPP1,ZFP36L1 |
| HALLMARK_PROTEIN_SECRETION | 1.2e-05 | 4.7e-05 | 554 | 96 | 8 | ARF1,BET1,KRT18,OCRL,RAB5A,TMED10,TOM1L1,YIPF6 |
| HALLMARK_COMPLEMENT | 1.7e-05 | 5.9e-05 | 554 | 200 | 11 | CDH13,CEBPB,CXCL1,IL6,IRF1,KYNU,L3MBTL4,PLAUR,PLEK,TFPI2,TNFAIP3 |
| HALLMARK_CHOLESTEROL_HOMEOSTASIS | 1.9e-05 | 6.2e-05 | 554 | 74 | 7 | CPEB2,JAG1,PLAUR,PNRC1,PPARG,STX5,TNFRSF12A |
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE | 4.0e-05 | 1.2e-04 | 554 | 113 | 8 | ATF6,CEBPB,DDIT4,HYOU1,IFIT1,PDIA5,VEGFA,XBP1 |
The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.
| gene_type | info |
|---|---|
| Dark Kinase (5) | CDK14, OBSCN, STK17A, STK17B, TSSK4 |
| Light Kinase (17) | AATK, BLVRA, GRK3, GRK4, MAP3K1, MAPK13, MET, MYO3B, NTRK3, OXSR1, PDK3, PIK3CD, PRKCI, RIPK4, SNRK, SYK, TNIK |
| Non-kinase Count | 550 |
| label | pval | fdr | signature | geneset | overlap | hits |
|---|---|---|---|---|---|---|
| HALLMARK_INFLAMMATORY_RESPONSE | 0.0e+00 | 0.0e+00 | 572 | 200 | 19 | BDKRB1,CCL22,CD55,CX3CL1,EBI3,IL10,IRF7,ITGB3,LCP2,LDLR,MET,NOD2,P2RX4,PTPRE,SERPINE1,TAPBP,TIMP1,TNFAIP6,TNFSF9 |
| HALLMARK_TNFA_SIGNALING_VIA_NFKB | 0.0e+00 | 0.0e+00 | 572 | 200 | 18 | BCL2A1,BCL6,FOS,FUT4,IL6ST,IRS2,LDLR,NFIL3,NR4A3,PDLIM5,PTPRE,SAT1,SDC4,SERPINE1,SOCS3,TIPARP,TNFAIP6,TNFSF9 |
| HALLMARK_HYPOXIA | 0.0e+00 | 0.0e+00 | 572 | 200 | 17 | AKAP12,ALDOC,ANGPTL4,ERRFI1,FOS,IRS2,ISG20,LARGE1,MAP3K1,MXI1,NFIL3,PDGFB,PDK3,SDC4,SERPINE1,TGM2,TIPARP |
| HALLMARK_CHOLESTEROL_HOMEOSTASIS | 0.0e+00 | 0.0e+00 | 572 | 74 | 11 | ALDOC,CXCL16,DHCR7,ERRFI1,HSD17B7,LDLR,MVD,MVK,NFIL3,PDK3,SQLE |
| HALLMARK_COMPLEMENT | 0.0e+00 | 0.0e+00 | 572 | 200 | 16 | CASP4,CBLB,CD55,CD59,CFH,DOCK4,DOCK9,IRF7,LCP2,LTA4H,PDGFB,PDP1,PHEX,SERPINE1,SIRT6,TIMP1 |
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION | 0.0e+00 | 1.0e-07 | 572 | 200 | 15 | CD59,EDIL3,ITGA2,ITGB3,ITGB5,MMP3,NT5E,SAT1,SDC4,SERPINE1,SERPINE2,SPP1,TGM2,TIMP1,VEGFC |
| HALLMARK_IL2_STAT5_SIGNALING | 1.0e-07 | 5.0e-07 | 572 | 199 | 14 | CCND2,DHRS3,FGL2,GLIPR2,IFNGR1,IL10,NFIL3,NT5E,P2RX4,SH3BGRL2,SHE,SLC29A2,SPP1,TGM2 |
| HALLMARK_INTERFERON_GAMMA_RESPONSE | 1.0e-07 | 5.0e-07 | 572 | 200 | 14 | CASP4,CFH,FGL2,HLA-B,IRF5,IRF7,ISG20,LCP2,PTPN1,SOCS3,SP110,TAPBP,TNFAIP6,TRIM25 |
| HALLMARK_KRAS_SIGNALING_UP | 1.0e-07 | 5.0e-07 | 572 | 200 | 14 | AKAP12,ALDH1A2,ANGPTL4,ANKH,CCND2,CFH,EPB41L3,GABRA3,ITGA2,ITGB2,MAP3K1,SPP1,TSPAN13,TSPAN7 |
| HALLMARK_UV_RESPONSE_DN | 1.0e-06 | 4.7e-06 | 572 | 144 | 11 | ADD3,CACNA1A,ICA1,INPP4B,ITGB3,LDLR,MET,PDLIM5,PIK3CD,SERPINE1,SYNJ2 |
| HALLMARK_ESTROGEN_RESPONSE_EARLY | 3.9e-06 | 1.8e-05 | 572 | 200 | 12 | ADD3,DEPTOR,DHCR7,DHRS3,FOS,GAB2,IL6ST,KRT15,MPPED2,PTGES,TGM2,TIPARP |
| HALLMARK_COAGULATION | 3.3e-05 | 1.4e-04 | 572 | 138 | 9 | CFH,ITGA2,ITGB3,LTA4H,MMP3,PDGFB,SERPINE1,SH2B2,TIMP1 |
| HALLMARK_IL6_JAK_STAT3_SIGNALING | 6.6e-05 | 2.5e-04 | 572 | 87 | 7 | CRLF2,EBI3,IFNGR1,IL6ST,ITGB3,PTPN1,SOCS3 |
| HALLMARK_ALLOGRAFT_REJECTION | 1.1e-04 | 3.4e-04 | 572 | 200 | 10 | CCL22,CCND2,CD28,IFNGR1,IL10,IRF7,ITGB2,LCP2,TAPBP,TIMP1 |
| HALLMARK_APOPTOSIS | 1.1e-04 | 3.4e-04 | 572 | 161 | 9 | ANKH,CASP4,CCNA1,CCND2,IFNGR1,ISG20,SAT1,SLC20A1,TIMP1 |
| HALLMARK_ESTROGEN_RESPONSE_LATE | 1.1e-04 | 3.4e-04 | 572 | 200 | 10 | ADD3,CCNA1,DHCR7,FOS,IL6ST,ISG20,LARGE1,MAPK13,PTGES,TSPAN13 |
| HALLMARK_P53_PATHWAY | 1.1e-04 | 3.4e-04 | 572 | 200 | 10 | APAF1,CCND2,FOS,HDAC3,PTPRE,RHBDF2,RRAD,SAT1,TM4SF1,TNFSF9 |
The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.
| gene_type | info |
|---|---|
| Dark Kinase (5) | CDC42BPA, CDK10, POMK, PSKH1, TSSK6 |
| Light Kinase (16) | CAMK1, CDK6, CHEK2, DCLK2, FASTK, LATS1, MAPK12, MAPK14, MOK, PIK3R4, PRKG2, RPS6KA4, RPS6KB2, STK25, TYK2, WNK4 |
| Non-kinase Count | 575 |
| label | pval | fdr | signature | geneset | overlap | hits |
|---|---|---|---|---|---|---|
| HALLMARK_OXIDATIVE_PHOSPHORYLATION | 0.0e+00 | 0.00000 | 596 | 200 | 18 | AFG3L2,ATP5MC3,ATP5MF,BAX,COX15,COX7B,ECHS1,MRPL34,NDUFA2,NDUFA3,NDUFB2,NDUFB7,NDUFC1,NDUFS2,NDUFS6,PMPCA,SDHA,UQCR10 |
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY | 2.5e-05 | 0.00054 | 596 | 49 | 6 | LSP1,MGST1,MSRA,NDUFS2,STK25,TXNRD2 |
| HALLMARK_ADIPOGENESIS | 3.2e-05 | 0.00054 | 596 | 200 | 11 | AGPAT3,CDKN2C,COX7B,DDT,ECHS1,MIGA2,NDUFB7,PFKL,SLC25A10,SNCG,UQCR10 |
The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.
| gene_type | info |
|---|---|
| Dark Kinase (4) | EEF2K, PKMYT1, PRPF4B, RSKR |
| Light Kinase (23) | AKT1, ATR, BUB1B, CDC7, CHUK, CIT, EPHA3, FASTKD1, FASTKD2, FASTKD3, FASTKD5, GRK6, HASPIN, MAP3K7, PBK, PI4K2B, PLK1, PRKDC, RPS6KA1, STRADB, TRIM28, TTK, VRK1 |
| Non-kinase Count | 1112 |
| label | pval | fdr | signature | geneset | overlap | hits |
|---|---|---|---|---|---|---|
| HALLMARK_E2F_TARGETS | 0.0e+00 | 0.0e+00 | 1139 | 200 | 84 | ASF1B,BARD1,BIRC5,BRCA1,BUB1B,CCNE1,CCP110,CDC20,CDCA3,CDCA8,CDKN3,CENPE,CIT,CKS1B,CKS2,CSE1L,DCLRE1B,DCTPP1,DLGAP5,DNMT1,DONSON,DSCC1,DUT,E2F8,EED,EXOSC8,GINS1,GINS3,H2AX,H2AZ1,HELLS,JPT1,KIF18B,KIF22,KIF4A,LBR,LIG1,LYAR,MAD2L1,MCM2,MCM5,MCM6,MKI67,MLH1,MRE11,MXD3,MYBL2,NCAPD2,NME1,NOP56,NUP107,ORC2,PA2G4,PAICS,PLK1,PNN,POLA2,POLD1,PPP1R8,PRKDC,PRPS1,PSIP1,PTTG1,RAD51C,RANBP1,RFC2,RFC3,RPA1,RPA3,RRM2,SMC1A,SMC6,SPAG5,SPC25,SSRP1,STMN1,SUV39H1,SYNCRIP,TACC3,TIMELESS,TK1,TRIP13,TUBG1,UBE2S |
| HALLMARK_G2M_CHECKPOINT | 0.0e+00 | 0.0e+00 | 1139 | 200 | 60 | BARD1,BIRC5,BUB3,CCNF,CDC20,CDC45,CDC7,CDKN3,CENPE,CENPF,CHAF1A,CKS1B,CKS2,DBF4,DTYMK,E2F4,EXO1,FANCC,FBXO5,H2AX,H2AZ1,H2AZ2,HIRA,JPT1,KIF11,KIF15,KIF20B,KIF22,KIF23,KIF4A,KNL1,LBR,MAD2L1,MCM2,MCM5,MCM6,MKI67,MTF2,MYBL2,NCL,NDC80,ORC5,PBK,PLK1,POLA2,POLQ,PRPF4B,PTTG1,SMC1A,SNRPD1,SRSF10,STIL,STMN1,SUV39H1,SYNCRIP,TACC3,TFDP1,TOP1,TTK,UBE2S |
| HALLMARK_MYC_TARGETS_V1 | 0.0e+00 | 0.0e+00 | 1139 | 200 | 58 | APEX1,BUB3,C1QBP,CAD,CDC20,CDC45,CLNS1A,CSTF2,DHX15,DUT,EIF1AX,EIF3B,EIF4E,ERH,FBL,GOT2,H2AZ1,HDAC2,HNRNPC,HNRNPR,HPRT1,HSPD1,HSPE1,LSM7,MAD2L1,MCM2,MCM5,MCM6,NCBP1,NDUFAB1,NME1,NOP16,NOP56,ORC2,PA2G4,PHB,POLE3,PPM1G,PRDX3,PRPS2,PTGES3,RANBP1,RFC4,SERBP1,SNRPD1,SNRPD3,SNRPG,SRM,SSB,SSBP1,STARD7,SYNCRIP,TFDP1,TOMM70,TRIM28,TXNL4A,TYMS,UBE2L3 |
| HALLMARK_MYC_TARGETS_V2 | 0.0e+00 | 0.0e+00 | 1139 | 58 | 21 | DCTPP1,HSPD1,HSPE1,IPO4,LAS1L,MCM5,MPHOSPH10,MRTO4,MYBBP1A,NOC4L,NOP16,NOP56,PA2G4,PHB,PLK1,PRMT3,SLC19A1,SRM,TCOF1,UTP20,WDR74 |
| HALLMARK_DNA_REPAIR | 0.0e+00 | 0.0e+00 | 1139 | 150 | 28 | BOLA2,CLP1,CSTF3,DUT,FEN1,GTF2A2,GTF2H3,GTF3C5,HPRT1,LIG1,NME1,POLA1,POLA2,POLD1,POLR1C,POLR2D,POLR2F,POLR2K,PRIM1,RFC2,RFC3,RFC4,RFC5,RPA3,SNAPC4,SSRP1,TYMS,UMPS |
| HALLMARK_MITOTIC_SPINDLE | 0.0e+00 | 0.0e+00 | 1139 | 199 | 30 | ANLN,ARAP3,BIRC5,CENPE,CENPF,CENPJ,CEP192,DLGAP5,ECT2,FBXO5,GEMIN4,KIF11,KIF15,KIF20B,KIF22,KIF23,KIF4A,KNTC1,NDC80,PIF1,PLEKHG2,PLK1,RHOT2,SASS6,SHROOM2,SMC1A,TTK,TUBA4A,TUBGCP3,TUBGCP5 |
| HALLMARK_MTORC1_SIGNALING | 0.0e+00 | 0.0e+00 | 1139 | 200 | 24 | ADIPOR2,CACYBP,CCNF,CTSC,DHFR,FDXR,HPRT1,HSPD1,HSPE1,MCM2,MTHFD2L,NUFIP1,PDAP1,PITPNB,PLK1,POLR3G,PSME3,PSPH,RPA1,RRM2,STIP1,TUBA4A,TUBG1,UCHL5 |
| HALLMARK_OXIDATIVE_PHOSPHORYLATION | 0.0e+00 | 0.0e+00 | 1139 | 200 | 22 | ATP5PF,COX11,CYCS,DLAT,FXN,GOT2,IDH3A,LDHB,MRPL11,MRPL35,MRPS12,MRPS22,NDUFAB1,OPA1,POLR2F,PRDX3,RHOT2,SDHB,SDHD,TIMM17A,TOMM22,TOMM70 |
| HALLMARK_UV_RESPONSE_UP | 3.7e-06 | 2.1e-05 | 1139 | 158 | 15 | AP2S1,CCNE1,CDC5L,CHRNA5,FEN1,FKBP4,H2AX,PDAP1,POLE3,POLG2,PPAT,RASGRP1,RFC4,STIP1,TUBA4A |
| HALLMARK_ADIPOGENESIS | 6.2e-05 | 3.1e-04 | 1139 | 200 | 15 | ADIPOR2,ATL2,ATP1B3,CHUK,CMBL,DHRS7B,DLAT,GPD2,IDH3A,NDUFAB1,PRDX3,PTCD3,SDHB,SLC19A1,SLC5A6 |
The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.
| gene_type | info |
|---|---|
| Dark Kinase (4) | BCKDK, PKN3, TBCK, TSSK3 |
| Light Kinase (15) | AKT2, BMPR1A, DDR1, DGKH, DGKI, HIPK2, IRAK1, MAP3K3, MAP4K3, PDPK1, PIK3CA, RIPK1, SIK2, TRRAP, WNK1 |
| Non-kinase Count | 394 |
| label | pval | fdr | signature | geneset | overlap | hits |
|---|---|---|---|---|---|---|
The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.
| gene_type | info |
|---|---|
| Dark Kinase (2) | MKNK2, NIM1K |
| Light Kinase (5) | DYRK1A, MAP3K2, PDK1, PRKAA2, TEC |
| Non-kinase Count | 390 |
| label | pval | fdr | signature | geneset | overlap | hits |
|---|---|---|---|---|---|---|
| HALLMARK_HYPOXIA | 0.0e+00 | 0.00000 | 397 | 200 | 33 | AK4,ALDOA,ANKZF1,BNIP3L,DPYSL4,EFNA3,ENO1,ENO2,ERO1A,F3,FAM162A,GAPDH,GLRX,GPI,IDS,IGFBP3,KLF7,LDHA,NDRG1,PDK1,PGF,PGK1,PLIN2,PPFIA4,PPP1R3C,RBPJ,RRAGD,SAP30,SLC2A3,SLC6A6,TPD52,TPI1,WSB1 |
| HALLMARK_GLYCOLYSIS | 0.0e+00 | 0.00000 | 397 | 200 | 27 | ABCB6,AK4,ALDOA,ANG,ANKZF1,DPYSL4,EFNA3,EGLN3,ENO1,ENO2,ERO1A,FAM162A,GLRX,GNE,IGFBP3,LDHA,ME1,NOL3,PGK1,PKM,PLOD1,PPFIA4,RRAGD,SAP30,SPAG4,TALDO1,TPI1 |
| HALLMARK_MTORC1_SIGNALING | 0.0e+00 | 0.00000 | 397 | 200 | 18 | AK4,ALDOA,EGLN3,ENO1,ERO1A,FADS1,GAPDH,GLRX,GPI,LDHA,ME1,MLLT11,PDK1,PGK1,PRDX1,SLC2A3,SLC6A6,TPI1 |
| HALLMARK_PROTEIN_SECRETION | 1.2e-05 | 0.00015 | 397 | 96 | 7 | AP2M1,AP3S1,BNIP3,GBF1,SCAMP1,SEC31A,TPD52 |
| HALLMARK_OXIDATIVE_PHOSPHORYLATION | 3.6e-05 | 0.00036 | 397 | 200 | 9 | ACADVL,BCKDHA,COX6B1,ETFA,GPI,LDHA,NDUFA6,NDUFA8,POR |
The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.
| gene_type | info |
|---|---|
| Dark Kinase (2) | PI4KA, RNASEL |
| Light Kinase (16) | BMPR2, CDK5, EPHA10, EPHB4, FPGT-TNNI3K, JAK3, MAP2K4, PDGFRB, PDK2, PIK3C2A, PRKD3, PTK7, ROCK1, SPEG, SRC, TRIM24 |
| Non-kinase Count | 435 |
| label | pval | fdr | signature | geneset | overlap | hits |
|---|---|---|---|---|---|---|
| HALLMARK_MITOTIC_SPINDLE | 2.4e-06 | 0.00012 | 453 | 199 | 11 | APC,ARHGEF11,CD2AP,CEP131,DLG1,DYNLL2,KIF3B,MID1,MYH9,ROCK1,TBCD |